HADDOCK: High Ambiguity Driven biomolecular DOCKing

The structure determination of protein-protein complexes is a rather tedious and lengthy
process, both by NMR and X-ray crystallography. Several methods based on docking to study
protein complexes have been well developed over the past few years. Most of these
approaches are however not driven by experimental data but based on combination of
energetics and shape complementarity.

HADDOCK (High
Ambiguity Driven biomolecular
DOCKing) is an approach that makes use of
biochemical and/or biophysical interaction data such as chemical shift perturbation data
resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.
This information is introduced as Ambiguous
Interaction Restraints
(AIRs) to drive the docking
process. An AIR is defined as an ambiguous distance between all residues shown to be
involved in the interaction.

The accuracy of our approach was initially demonstrated using NMR titration data for three
protein-protein complexes. Since the original 2003 JACS publication, HADDOCK has been
extended to deal with a large variety of data and types of complexes and has shown a strong
performance in the CAPRI blind docking experiment. Next to protein-protein docking,
HADDOCK has been widely applied to the modelling of protein-DNA, protein-RNA, protein-
oligosaccharides and protein-ligand complexes. A friendly user interface has been developed
within Extend-NMR that provides control on the docking parameters and allows a simple launch
of the calculations via the HADDOCK web portal.

A: Manage multiple projects with ease

C: Full control over ALL the settings of a HADDOCK run

B: Convenient setup and control of Ambiguous Interaction Restraints and flexibility

D: Various export capabilities to run your job on your own computational
infrastructure or have our servers run it for you (requires a subscription, http://haddock.chem.uu.nl )

HADDOCK Features

Support for various experimental restraint type

Easy use of diverse biochemical data to drive the docking

User-friendly web portal

Support for proteins, nucleic acids, oligosaccharides and small ligands